The host innate immune response is triggered within hours of virus infection. As a whole, its function is to limit virus replication at local sites of infection and to orchestrate development of the adaptive immune response. Viruses are typically recognized by cellular pattern recognition receptors (PRRs), including toll-like receptors (TLRs) and the retinoic acid inducible gene (RIG)-like RNA helicases (RLHs). Ligation of these PRRs, often by viral nucleic acids, culminates in the activation of multiple transcription factors that cooperate in driving expression of cytokines and chemokines characteristic of the innate response. Nuclear factor-kappa B (NF-kappaB) and interferon (IFN) regulatory factors (IRFs) are particularly important transcription factors, responsible for induction of type I IFN (IFNalpha/beta), tumor necrosis factor alpha (TNFalpha) and other mediators of inflammation. IFNalpha/beta is central to the anti-viral response as it initiates its own transcriptional program resulting in expression of IFN-stimulated genes (ISGs) via the Janus kinase-signal transducer and activation of transcription (JAK-STAT) pathway. ISG expression influences many cellular processes including RNA processing, protein stability and cell viability that can directly affect virus replication. ISG expression in cells of the immune system such as dendritic cells (DCs) and macrophages is critical for antigen presentation and T- and B-cell activation, thus affecting the quality of the adaptive immune response and eventual virus clearance. To facilitate dissemination, pathogenic viruses have evolved mechanisms to suppress host innate immunity by antagonizing these signal transduction pathways. Hence, understanding the specific pathways by which viruses activate and evade innate immune responses is essential for understanding viral pathogenesis as well as for development of effective vaccines. To examine virus-host interactions that affect innate immunity, our laboratory utilizes flaviviruses as the primary model of infection. Flaviviruses have an essentially global distribution and represent a tremendous disease burden to humans, causing millions of infections annually. The success of flaviviruses as human pathogens is associated with the fact that they are arthropod-borne, transmitted by mosquitoes or ticks. Significant members of this group include dengue virus (DENV) and yellow fever virus (YFV) that cause hemorrhagic fevers, as well as Japanese encephalitis virus (JEV), West Nile virus (WNV), tick-borne encephalitis virus (TBEV) and most recently Zika virus (ZIKV) that cause infections of the central nervous system. These viruses are listed as NIAID category A, B and C pathogens for research into their basic biology and host response. The flavivirus single-stranded RNA genome is translated as one open reading frame; the resulting polyprotein is cleaved into at least ten proteins that include three structural (capsid C, membrane M, derived from the precursor preM and envelope E), and seven nonstructural proteins (NS1, NS2A, NS2B, NS3, NS4A, NS4B and NS5). Virus replication proceeds in association with modified membranes derived from the endoplasmic reticulum of host cells. NS5 is the largest and most conserved of the flavivirus proteins containing approximately 900 amino acids. It encodes a methyltransferase (MTase) and RNA-dependent RNA polymerase (RdRP) and associates with NS3 (the viral protease) to form the functional unit of the viral replication complex. Despite the widespread and often severe infections caused by these pathogens, vaccines exist for only a few (YFV, JEV and TBEV) and no therapeutic exists to treat clinical infection caused by any flavivirus. Type I IFNs are essential to recovery from flavivirus infection and have been used clinically as potential therapeutics, albeit with limit success. This may be due to the observation that all flaviviruses examined to date antagonize IFN-dependent responses by suppressing JAK-STAT signal transduction. We identified NS5 as the major IFN antagonist encoded by flaviviruses, originally using Langat virus (LGTV; a member of the TBEV complex of flaviviruses) and more recently using WNV. Although other NS proteins contribute to suppression of JAK-STAT signaling, studies by our laboratory and others suggest that NS5 is the most potent of the IFN antagonist proteins encoded by all vector-borne flaviviruses examined thus far. Hence, determining the mechanism(s) by which NS5 impedes signaling is essential to understand flavivirus pathogenesis and may lead to new therapeutic targets. Furthermore, it is important to understand the mechanisms underlying the anti-viral effects of IFN by identifying the function of ISGs with anti-viral activity. Finally, it is essential to translate these findings to immunologically relevant cell types and animal models to understand the roles of induction and evasion of innate immunity in development of the adaptive immune response and in virus pathogenesis. Achieving these goals will significantly improve our understanding of how viruses emerge and cause disease in humans, as well as identify therapeutic targets for intervention. One major area of work in the lab is to understand the role of Zika virus NS5 in evasion of IFN signaling. As part of this work, we have found interactions between NS5 and mitochondrial proteins that is leading to a better understanding of mitochondria in the IFN responses. We also collaborated with Dr. Adolfo Garcia-Sastre (Icahn School of Medicine at Mt Sinai) to show that the NS5 protein of Zika virus degrades STAT2 to escape IFN signaling. However, the relative ability to do this is host-species restricted, which explains in part the need to compromise the IFN response in mouse models in order to observe disease. To overcome these limitations, we are developing a number of animal models to examine Zika virus pathogenesis. The second major area of research is determining how genes induced by type I interferon, called ISGs, confer virus-specific protection. We have found a surprising new role for TRIM proteins in flavivirus-specific host protection. We are now using new animal models to determine the role of these proteins in vivo and to determine if selective pressure from TRIM proteins is sufficient to drive flavivirus evolution and emergence. A third emphasis in the lab is the understanding of cell-type specific RLR signaling in host resistance to virus infection. We are using our floxed mouse model of conditional deletion of the MAVS gene. MAVS is an essential adaptor protein that connects the ligation of RIG-I-like RNA helicases by viral RNA to the expression of type I IFN. The conditional deletion of MAVS (MAVSfl/fl) enables selective depletion of this pathway in specific cell types such as macrophages and dendritic cells. Although we most commonly study flaviviruses, the unprecedented 2013-2016 outbreak of Ebola virus (EBOV) resulted in over 11,300 human deaths and necessitated additional work into host responses and so we applied EBOV to this mouse model. We applied a systems approach to MAVS-/- mice infected with either wild-type or mouse-adapted EBOV which revealed how MAVS controls EBOV replication through the expression of IFN, regulation of inflammatory responses in the spleen, and prevention of cell death in the liver. We are now using single-cell technologies to determine how RLR-MAVS signaling orchestrates protective antiviral responses in vivo.